Linker histones (LHs) bind to linker DNA, protecting ~20-bp DNA at nucleosome entry/exit points and promoting formation of the 30-nm fiber. Earlier studies showed that LHs exhibit relatively weak preference for AT-rich DNA [1]. However, it was unclear whether there are any sequence patterns facilitating LH binding. These patterns (if they exist) are expected to be more pronounced in metazoan nucleosomes with abundant LHs, compared to yeast nucleosomes with few LHs.

To test this hypothesis, we compared the nucleosome core particle (NCP) sequences with single-nucleotide resolution from chicken [2], Drosophila [3] and yeast [4, 5], extending them by the flanking sequences extracted from the corresponding genomes. We found that the known ~10-bp periodic oscillation of AT-rich elements goes beyond the ends of yeast nucleosomes, but is distorted in the chicken and Drosophila sequences where the ?out-of-phase? AT-peaks appear at the NCP ends. We therefore suggest that the observed difference in the occurrence of AT-rich fragments at the ends of metazoan and yeast nucleosomes may reflect distinctive spatial trajectories of DNA at the entry/exit points, which could be related to LH binding.

Based on these findings, we propose a new structural model for LH binding to metazoan nucleosomes based on the X-ray structure of chicken H5 globular domain (GH5), postulating that the highly conserved non-polar ?wing? region of the LH globular domain (tetrapeptide GVGA) recognizes AT-rich fragments through hydrophobic interactions with the thymine methyl groups. These interactions lead to DNA bending at the NCP ends and formation of a ?stem-like? structure. The detailed energy minimization of the GH5-NCP complex suggests that the valine in the ?wing? domain can favorably interact with thymines in both DNA strands at the ends of nucleosomes. Preliminary experimental results (in collaboration with Dr. Sergei Grigoryev at Pennsylvania State University) are consistent with our model, showing that the AT-rich fragments at the nucleosome ends are indeed critical for strong LH binding.

Our model explains and links together several key observations made earlier:

1. additional deformation of nucleosomal DNA caused by linker histone binding;
2. formation of the stem-like structure in the presence of LH;
3. preferential LH binding to AT-rich DNA;
4. stronger binding of H1⁰/H5 histones compared to somatic H1a, b, c? variants;
5. preferential LH binding to methylated DNA and stabilization of ?epigenetic? heterochromatin.

Finally, we found that AT-rich fragments frequently occur near the ends of well-positioned nucleosomes in higher eukaryotes, for example, in human Alu repeats and in African Green Monkey α-satellite DNA. We suggest that these structurally-rigid, nucleosome-excluding fragments may be recognized by LHs. These LH-related sequence patterns could provide additional information for predicting nucleosome positioning in vivo.

References and Footnotes

1. Zlatanova, J. and van Holde, K. Prog. Nucleic Acid Res. Mol. Biol. 52, 217-259 (1996).
2. Satchwell, S.C., Drew, H.R. and Travers, A.A. J. Mol. Biol. 191, 659-675 (1986).
3. Mavrich, T.N., Jiang, C., Ioshikhes, I.P., Li, X., Venters, B.J., Zanton, S.J., Tomsho, L.P., Qi, J., Glaser, R.L., Schuster, S.C., Gilmour, D.S., Albert, I. and Pugh, B.F. Nature 453, 358-362 (2008).
4. Segal, E., Fondufe-Mittendorf, Y., Chen, L, Thastrom, A., Field, Y., Moore, I.K., Wang, J.P. and Widom, J. Nature 442, 772-778 (2006).
5. Albert, I., Mavrich, T.N., Tomsho, L.P., Qi, J., Zanton, S.J., Schuster, S.C. and Pugh, B.F. Nature 446, 572-576 (2007).